4,369 research outputs found
phenoscape/phenoscape-kb-services: Release 2.0
No full textWhat's Changed
Enables Docker build for this application by @hlapp in https://github.com/phenoscape/phenoscape-kb-services/pull/52
Query by publications by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/54
Restore TSV output for taxon list output by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/60
Implement preliminary service providing Jaccard similarity score for a pair of character states by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/61
Add missing import. by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/62
Correct services to ignore limit if <1. by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/65
Update from swagger hub to fix study query doc. by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/66
Service for pairwise similarity of list of ontology classes by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/67
Include entity in OntoTrace query including its parts. by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/71
Generated code by SwaggerHub by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/72
Generated code by SwaggerHub by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/74
Created service for computing ancestor matrix by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/75
Issue 77 by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/78
Document subsumer matrix service. by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/79
Make sort case-insensitive by @Shalsh23 in https://github.com/phenoscape/phenoscape-kb-services/pull/80
Swaggerhub by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/84
Update matrix service to take JSON array of IRIs. by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/85
Generated code by SwaggerHub by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/86
Generated code by SwaggerHub by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/88
Support POST for OntoTrace. by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/87
Swaggerhub by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/96
Generated code by SwaggerHub by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/97
Generated code by SwaggerHub by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/99
Generated code by SwaggerHub by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/100
Make ic_disparity query parameter names consistent. by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/101
Generated code by SwaggerHub by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/102
Return matrix for study as application/xml. by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/103
Added method for executing SPARQL ASK queries. by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/105
Generated code by SwaggerHub by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/107
Generated code by SwaggerHub by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/108
Implement services to handle queries for inferred presence/absence. by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/110
New presence absence matrix branch by @Shalsh23 in https://github.com/phenoscape/phenoscape-kb-services/pull/111
Generalize term search. by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/115
Generated code by SwaggerHub by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/117
Generated code by SwaggerHub by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/118
Generated code by SwaggerHub by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/120
Accept JSON array for definedBy. by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/119
Add ui button to get dependency matrix by @Shalsh23 in https://github.com/phenoscape/phenoscape-kb-services/pull/114
Merge master by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/123
Fix query parameter name by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/124
Fix space in sample data. by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/125
Update media type to text/csv. by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/126
Boost match rank of terms with text exactly equal to search text. by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/131
Return only one label for ancestor and descendant queries. Fixes #129. by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/132
Add newline in results EOF by @Shalsh23 in https://github.com/phenoscape/phenoscape-kb-services/pull/133
Provide option to make use of part_of for ancestor and descendant queries. by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/134
Swaggerhub by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/135
Fixes typos in /similarity/matrix documentation by @hlapp in https://github.com/phenoscape/phenoscape-kb-services/pull/140
Use correct media type for ancestor matrix service by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/142
Add POST to /term/labels and /entity/dependency services by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/143
Implement service providing frequency information for an ontology term according to some identified corpus by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/151
Allow caching of POST requests. by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/152
Preserve user specified order of iris in dependency matrix by @Shalsh23 in https://github.com/phenoscape/phenoscape-kb-services/pull/150
Support streaming response for TaxonPhenotypeAnnotations TSV (and more) by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/153
Add documentation for taxon annotations query and annotation sources query. by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/155
Document publication parameter. by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/158
Return character id and label in the results of the study/phenotype kb-service by @Shalsh23 in https://github.com/phenoscape/phenoscape-kb-services/pull/156
Accept JSON arrays for all IRI lists. by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/159
Enable content negotiation with streaming annotations response. by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/160
Migrate matrix renderer test to utest by @Shalsh23 in https://github.com/phenoscape/phenoscape-kb-services/pull/164
Fix #26: Annotate ontotrace matrix with variable status by @Shalsh23 in https://github.com/phenoscape/phenoscape-kb-services/pull/166
Order text search results consistently for different values of limit by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/168
Document acceptance of json array of IRIs for kb services by @Shalsh23 in https://github.com/phenoscape/phenoscape-kb-services/pull/169
Make character IRI and label available where needed. by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/178
Combine character id and label into a single json object by @Shalsh23 in https://github.com/phenoscape/phenoscape-kb-services/pull/180
Issue 139 - merge term labels by @Shalsh23 in https://github.com/phenoscape/phenoscape-kb-services/pull/170
Add 'phenotype' parameter to query endpoints. For issue #148. by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/181
Implement phenotype info service. by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/185
Refinements to phenotype info service. by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/186
Document phenotype info service. by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/187
Retrieve dependency matrix with a single query. by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/204
Fixes #167: Adds missing author to ontotrace matrix by @Shalsh23 in https://github.com/phenoscape/phenoscape-kb-services/pull/205
Add implementation for similarity/frequency for genes corpus by @Shalsh23 in https://github.com/phenoscape/phenoscape-kb-services/pull/206
Return null if label doesn't exist by @Shalsh23 in https://github.com/phenoscape/phenoscape-kb-services/pull/209
Only show states that are linked to taxon in /phenotype/info. by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/208
Update sparql-interpolator. by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/213
Return only one label for a term. by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/211
Convert None responses for Option values into 404. by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/212
Change MinimalTerm label to Option[String]. by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/214
Fix null pointer exception in query result. by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/215
Update sbt to 1.3.8 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/235
Update scalaz-core to 7.2.30 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/236
Update scowl to 1.3.4 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/234
Update phenoscape-kb-ingest to 1.6.2 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/233
Update groovy-all to 2.4.19 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/231
Update apache-jena-libs to 3.14.0 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/230
Update owlapi-distribution to 4.2.9 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/229
Update sbt-native-packager to 1.3.25 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/226
Update utest to 0.7.4 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/223
Update scala. Remove guava. by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/237
Update sbt-native-packager to 1.7.0 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/238
Update groovy-all to 2.5.10 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/240
Update owlapi-distribution to 4.5.15 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/239
Update commons-io to 2.6 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/227
Update to JavaConverters, remove warnings. by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/241
Update akka-stream-alpakka-xml to 1.1.2 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/222
Update owlet to 1.6.2 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/232
Update akka-actor, akka-slf4j, akka-stream to 2.5.30 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/224
Update spray-json to 1.3.5 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/228
Update akka-http-cors to 0.3.4 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/219
Update logback-classic to 1.1.11 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/220
Update results json in api docs by @Shalsh23 in https://github.com/phenoscape/phenoscape-kb-services/pull/248
Update akka-actor, akka-slf4j, akka-stream to 2.6.4 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/246
Update akka-http-cors to 0.4.2 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/244
Update logback-classic to 1.2.3 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/245
Update akka-http, akka-http-caching, ... to 10.1.11 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/225
Update owlet to 1.7 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/247
Fix missing results in ancestors & descendants services by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/218
Return 0 count for frequency query when term is not matched in SPARQL query by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/216
Include character, state, and cell IRIs in matrix output. by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/217
Fixes #188: Return term source ontology by @Shalsh23 in https://github.com/phenoscape/phenoscape-kb-services/pull/249
Update sbt to 1.3.9 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/250
Remove println by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/251
Update groovy-all to 2.5.11 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/253
Update sbt to 1.3.10 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/255
Update owlet to 1.8.1 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/259
Update akka-http-cors to 0.4.3 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/256
Update owlapi-distribution to 4.5.16 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/257
Issue 179 kb metadata by @Shalsh23 in https://github.com/phenoscape/phenoscape-kb-services/pull/252
Update sbt-native-packager to 1.7.1 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/264
Update akka-actor, akka-slf4j, akka-stream to 2.6.5 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/263
Add synonym detail to taxon info by @Shalsh23 in https://github.com/phenoscape/phenoscape-kb-services/pull/266
Fix some deprecation warnings. by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/265
Reformat with new scalafmt configs by @Shalsh23 in https://github.com/phenoscape/phenoscape-kb-services/pull/271
Update to new sparql-utils. by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/276
Change scalafmt align setting by @Shalsh23 in https://github.com/phenoscape/phenoscape-kb-services/pull/283
Update akka-http, akka-http-caching, ... to 10.1.12 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/269
Update apache-jena-libs to 3.15.0 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/273
Update groovy-all to 2.5.12 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/275
Update Scala version for Travis by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/285
Update sbt-native-packager to 1.7.2 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/270
Test automatic SPARQL result derivation. by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/279
Update akka-actor, akka-slf4j, akka-stream to 2.6.6 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/291
Update akka-stream-alpakka-xml to 2.0.1 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/292
Update scalafmt-core to 2.5.3 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/278
Update sbt-native-packager to 1.7.3 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/289
Update sbt to 1.3.12 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/288
Update commons-io to 2.7 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/284
Update scalafmt-core to 2.6.0 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/293
Update akka-http-cors to 1.0.0 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/277
Make tests actually run. by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/295
Update scalafmt-core to 2.6.1 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/296
Change phenotypic profiles method to work with the new monarch schema by @Shalsh23 in https://github.com/phenoscape/phenoscape-kb-services/pull/183
Updates for new Gene model by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/297
Update owlapi-distribution to 4.5.17 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/301
Update sbt to 1.3.13 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/299
Update sbt-native-packager to 1.7.4 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/302
Update apache-jena-libs to 3.16.0 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/306
Update scalafmt-core to 2.6.4 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/308
Update groovy-all to 2.5.13 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/309
Update akka-actor, akka-slf4j, akka-stream to 2.6.8 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/307
Update groovy-all to 3.0.5 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/311
Fixes #90 - add option to include subclasses, or not, for entity and … by @Shalsh23 in https://github.com/phenoscape/phenoscape-kb-services/pull/290
Update sbt to 1.4.0 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/335
Update scalafmt-core to 2.7.5 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/341
Bug fix; rewrite query using sparql interpolator by @Shalsh23 in https://github.com/phenoscape/phenoscape-kb-services/pull/344
Update sbt-native-packager to 1.7.6 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/340
Update owlapi-distribution to 4.5.18 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/345
Update sbt to 1.4.1 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/343
Update commons-io to 2.8.0 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/322
Update utest to 0.7.5 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/318
Update sbt to 1.4.4 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/356
Update utest to 0.7.7 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/375
Update scalaz-core to 7.2.31 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/373
Don't return owl:Thing in ancestor results. by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/383
Update sbt to 1.4.7 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/381
Update sbt-native-packager to 1.8.0 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/369
Update akka-actor, akka-slf4j, akka-stream to 2.6.12 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/379
Update sparql-utils, sparql-utils-owlapi to 1.3 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/360
Update spray-json to 1.3.6 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/350
Roll back changes to taxon info return format. by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/384
Create scala.yml by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/385
Update scala.yml by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/386
Services new data model by @Shalsh23 in https://github.com/phenoscape/phenoscape-kb-services/pull/329
Update scala-library to 2.12.13 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/394
Allow return of all search results using limit < 1. by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/395
Update sparql-utils, sparql-utils-owlapi to 1.3.1 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/396
Update apache-jena-libs to 3.17.0 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/357
Update akka-http, akka-http-caching, ... to 10.1.14 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/392
Update akka-stream-alpakka-xml to 2.0.2 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/327
Support search and info for genes without phenotype annotations in switch to Monarch data. by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/399
Full Changelog: https://github.com/phenoscape/phenoscape-kb-services/compare/v0.5...v2.
Monseremus bellus Tan & Japir & Chung & Robillard 2022, new combination
No full textMonseremus bellus (Tan & Wahab, 2018) new combination (Figs 2D–F, 3C, 3D) Melaneremus? bellus Tan & Wahab, 2018: 584 Melaneremus (?) sp. — Tan & Wahab, 2018b: 132 Melaneremus bellus — Cadena-Castañeda 2019: 79 Material examined. Holotype: BRUNEI DARUSSALAM:• ♀; Ulu Temburong National Park, Kuala Belalong Field Studies Centre, primary ridge dipterocarp forest; N4.54731, E115.15697, 103.9± 8.7 m.a.s.l.; on foliage of tree; 26 July 2017, 20h31; coll. M. K. Tan (KB.17.76, ZRC). Paratypes: BRUNEI DARUSSALAM: • 1♀; Ulu Temburong National Park, Kuala Belalong Field Studies Centre, primary ridge dipterocarp forest; N4.54629, E115.15680, 133.9±9.0 m.a.s.l.; on rattan leaf; 23 September 2016; 21h49; coll. M. K. Tan (KB.16.20, ZRC) • 1♂; Ulu Temburong National Park, Kuala Belalong Field Studies Centre, primary ridge dipterocarp forest; N4.54706, E115.15720, 112.1±16.0 m.a.s.l.; on foliage of tree; 23 September 2016, 22h14; coll. M. K. Tan (KB.16.22, ZRC) • 1♂; Ulu Temburong National Park, Kuala Belalong Field Studies Centre, primary ridge dipterocarp forest; N4.54584, E115.15685, 103.3± 6.8 m.a.s.l., on foliage near ground; 25 July 2017, 21h30; coll. M. K. Tan (KB.16.63, ZRC) • 1♀; Ulu Temburong National Park, Kuala Belalong Field Studies Centre, primary ridge dipterocarp forest; N4.54730, E115.15703, 99.8±6.0 m.a.s.l.; on rattan leaf; 26 July 2017, 20h41; coll. M. K. Tan (KB.17.77, ZRC) • 1♂; Ulu Temburong National Park, Kuala Belalong Field Studies Centre, primary ridge dipterocarp forest; N4.54655, E115.15688, 101.9± 7.5 m.a.s.l.; on rattan leaf; 27 July 2017, 20h38; coll. M. K. Tan (KB.17.90, ZRC). Revised diagnosis. The male differs from that of M. appendiculatus by the medial processes of the tenth abdominal tergite: the inner margins and apices touching each other. The female differs from that of M. appendiculatus by the projections at the anterior margin of subgenital plate smaller, more flattened (in lateral view), and shorter in length than subgenital plate. Other minor differences include the male subgenital plate more transverse, ca. 2.5 times wider than long; the ovipositor <16.5 mm in length, shorter than M. appendiculatus. Distribution. BRUNEI DARUSSALAM: Temburong Ecology. This species is currently known to inhabit the lowland ridge dipterocarp forest.Published as part of Tan, Ming Kai, Japir, Razy, Chung, Arthur Y. C. & Robillard, Tony, 2022, A review of the genus Monseremus Ingrisch, 2018 (Orthoptera, Stenopelmatoidea Gryllacrididae) from Borneo, pp. 107-114 in Zootaxa 5165 (1) on pages 112-113, DOI: 10.11646/zootaxa.5165.1.5, http://zenodo.org/record/682565
Cercoteratura mirabilis Tan & Wahab 2020, comb. nov.
No full textCercoteratura mirabilis (Tan & Wahab, 2018) comb. nov. (Fig. 2) Kuzicus mirabilis — Tan & Wahab, 2018a: 583> original description. Tan & Wahab, 2018b: 137> record in Kuala Belalong Field Studies Centre Type details. Male holotype (Universiti Brunei Darussalam Museum, Brunei), Borneo, Brunei, Ulu Temburong National Park, Kuala Belalong Field Studies Centre Material examined. Holotype (male, KB.17.93): Brunei Darussalam, Ulu Temburong National Park, Kuala Belalong Field Studies Centre along Ashton Trail, primary ridge dipterocarp forest, N4.54595, E115.15700, 126.2± 9.4 m.a.s.l., under foliage of tree, 27 July 2017, 2120 hours, coll. M. K. Tan (dried pinned). Male (collected as subadult but did not emerge into adult properly) (KB.19.36), same locality as holotype, N4.54589, E115.15690, 120.5± 8.9 m.a.s.l., under foliage of tree, 16 July 2019, 1951 hours, coll. M. K. Tan & H. Yeo. Generic status. The species is considered a member of Cercoteratura by the presence of these characters: male tenth abdominal tergite with posteromedian lobe (which is rather diverse in shape and width among congeners), male cerci strongly curved upwards and situated very close to each other in rest position (sensu Gorochov, 2019). Comparison with congeners and diagnosis. Cercoteratura mirabilis comb. nov. differs from all known congeners by (1) male tenth abdominal tergite with posterior margin deeply notched in the middle, in the middle produced into a flat rectangular lobe; apex of this rectangular lobe with two lateral stout processes. (2) Basal part of male cercus laterally produced into a triangular ventral lobe pointing externally and with a small flattened ventral internal lobe; remaining of cercus curved dorsad, then anteriorly; apex of cercus somewhat truncated, sinuate into a flattened apical lobe pointing internally when viewed posteriorly. (3) Male genitalia with elongated sclerotized epiphallus; lateral margin with a lobe at the middle and ventro-posterior end; lateral lobes produced into acute spinelike processes (Tan & Wahab, 2018b). Cercoteratura mirabilis comb. nov. is most similar to C. spinicauda and C. variegata by the black patterns across the body (whereas C.? abbreviata and C. modesta are more unicolourous) but the males differs mainly by shape of tenth abdominal tergite, shape of cercus and genitalia.Published as part of Tan, Ming Kai & Wahab, Rodzay Bin Haji Abdul, 2020, A short taxonomic note on the katydids from the genus Cercoteratura Gorochov, 2019 (Orthoptera: Tettigoniidae: Meconematinae), with a key to species, pp. 591-595 in Zootaxa 4750 (4) on page 593, DOI: 10.11646/zootaxa.4750.4.10, http://zenodo.org/record/370879
Ectatoderus nigrofasciatus Tan & Wahab 2021
No full textEctatoderus nigrofasciatus Tan & Wahab, 2021 (Fig. 3) Ectatoderus nigrofasciatus Tan et al., 2021: 412 Ectatoderus nigrofasciatus — Tan et al. 2022b: 600 Ectatoderus sp. — Tan & Wahab 2018: 132 Specimen examined. Holotype: BRUNEI DARUSSALAM • ♂; Belait District, Jalan Labi near Andulau Forest Reserve, N4.63354, E114.51047, 76.6±5.0 m.a.s.l.; 7 July 2019, 20h42; on rattan foliage; coll. M.K. Tan; BRU.19.70 (UBDM) Additional specimens examined. BRUNEI DARUSSALAM • 1♂; Temburong District, Kuala Belalong Field Studies Centre, along Sungei Mata Ikan, N4.54742, E115.15715, 73.8± 27.9 m.a.s.l.; 22 September 2016, 22h33; on a foliage of a tree after rain; coll. M.K. Tan; KB.16.4 (ZRC) • 1♂; Temburong District, Kuala Belalong Field Studies Centre, along Sungei Mata Ikan, N4.54733, E115.15720, 113.4± 14.2 m.a.s.l.; 23 September 2016, 19h00; on a foliage of a tree after rain; coll. M.K. Tan; KB.16.15 (ZRC) Remarks. When Ectatoderus nigrofasciatus Tan et al., 2021 was first described, the basal part of the male genitalia of the holotype was not examined (Tan et al., 2021: Fig. 7). The apical part of the male genitalia, previously thought to be the complete genitalia, was considered to resemble that of Ectatoderus argentatus Ingrisch, 2006 from Thailand. However, after examining more specimens collected from Brunei Darussalam, it was found that the basal half of the male genitalia of E. nigrofasciatus has in fact the medial valve curved to a spiral. This character is more similar to that in Ectatoderus angusticollis Chopard, 1969 from Singapore (Fig. 3). Below, the diagnosis is revised accordingly. Revised diagnosis. The species is characterised by the scapus being dorsally black, but ventrally and laterally brown, and the antennae being entirely black basally; the head has a distinct black band behind eyes; and the male phallic complex is very large and forming a spiral. The new species is most similar and closest in distribution to E. angusticollis. In both species, the pronotum is more strongly widening toward apex, and the TIs and TIIs are provided with black dorsal stripes. The male phallic complex is very similar to that of E. angusticollis, including the spiral-shaped medial valve and the shape of the ventro-external sclerite. The species differs from E. angusticollis by the male phallic complex being exceptionally larger despite of having very similar body size (Fig. 3); the scapus and antennae being black (instead of testaceous); and the head being provided with distinct black and white bands behind eyes. The new species is also similar to E. argentatus having the pronotum strongly widening apically and the frons dark; it differs by the scapus and basal antennal segments being darkened instead of yellowish brown, and by the male phallic complex forming a spiral at base instead of being merely curved. Distribution. Borneo, BRUNEI DARUSSALAM: Belait and Temburong [new locality record] Districts Type locality. BRUNEI DARUSSALAM, Belait District, near Andulau Forest ReservePublished as part of Tan, Ming Kai, Japir, Razy, Chung, Arthur Y. C., Wahab, Rodzay Bin Haji Abdul & Robillard, Tony, 2022, Taxonomy and bioacoustics of scaly crickets (Orthoptera, Mogoplistidae Mogoplistinae) from Borneo and Singapore, pp. 177-189 in Zootaxa 5213 (2) on pages 181-182, DOI: 10.11646/zootaxa.5213.2.6, http://zenodo.org/record/735437
PDBe-KB: collaboratively defining the biological context of structural data
No full textThe Protein Data Bank in Europe – Knowledge Base (PDBe-KB, https://pdbe-kb.org) is an open collaboration between world-leading specialist data resources contributing functional and biophysical annotations derived from or relevant to the Protein Data Bank (PDB). The goal of PDBe-KB is to place macromolecular structure data in their biological context by developing standardised data exchange formats and integrating functional annotations from the contributing partner resources into a knowledge graph that can provide valuable biological insights. Since we described PDBe-KB in 2019, there have been significant improvements in the variety of available annotation data sets and user functionality. Here, we provide an overview of the consortium, highlighting the addition of annotations such as predicted covalent binders, phosphorylation sites, effects of mutations on the protein structure and energetic local frustration. In addition, we describe a library of reusable web-based visualisation components and introduce new features such as a bulk download data service and a novel superposition service that generates clusters of superposed protein chains weekly for the whole PDB archive.ELIXIR [IDP implementation study]; Biotechnology and Biological Sciences Research Council via the 3D-Gateway [BB/T01959X/1]; FunPDBe [BB/P024351/1]; European Molecular Biology Laboratory-European Bioinformatics Institute who supported this work; J.D. acknowledges support from the Ministry of Education, Youth and Sport of the Czech Republic [INBIO CZ.02.1.01/0.0/0.0/16_026/0008451]; R.S., K.B. and J.D. also acknowledge support from the Ministry of Education, Youth and Sport of the Czech Republic [ELIXIR-CZ LM2018131]; L.M. acknowledges support from the European Union's Horizon 2020 Programme (H2020-INFRAIA-2018-1) [823839]; Research Foundation Flanders (FWO) [G032816N, G042518N, G028821N]; W.V. acknowledges support from the Research Foundation Flanders (FWO) [G032816N, G028821N]; A.R. acknowledges support from the Fondazione Cassa Di Risparmio di Firenze [24316]; European Commission [101017567]; M.H.C. acknowledges the AIRC project to MHC [IG 23539]; J.F.-R. acknowledges support from the Spanish Ministry of Science and Innovation [PID2019-110167RB-I00]; N.R. acknowledges support from the Norwegian Research Council (Norges Forskningsråd) [288008]; E.D.L. acknowledges support from the European Union's Horizon 2020 research and innovation programme [819318]; M.J.E.S. acknowledges support from the Wellcome Trust [104955/Z/14/Z, 218242/Z/19/Z]. Funding for open access charge: Biotechnology and Biological Sciences Research Council grant [BB/T01959X/1]; Wellcome Trust [104955/Z/14/Z and 218242/Z/19/Z].Peer ReviewedCurrent PDBe-KB Consortium Members with Affiliations. (BSC author: Gonzalo Parra)
Mihaly Varadi1, Stephen Anyango, David Armstrong, John Berrisford, Preeti Choudhary, Mandar Deshpande, Nurul Nadzirin, Sreenath S. Nair, Lukas Pravda, Ahsan Tanweer, Bissan Al-Lazikani, Claudia Andreini, Geoffrey J. Barton, David Bednar, Karel Berka, Tom Blundell, Kelly P Brock, Jose Maria Carazo, Jiri Damborsky, Alessia David, Sucharita Dey, Roland Dunbrack, Juan Fernandez Recio, Franca Fraternali, Toby Gibson, Manuela Helmer-Citterich, David Hoksza, Thomas Hopf, David Jakubec, Natarajan Kannan, Radoslav Krivak, Manjeet Kumar, Emmanuel D Levy, Nir London, Jose Ramon Macias, Madhusudhan M. Srivatsan, Debora S Marks, Lennart Martens, Stuart A McGowan, Jake E McGreig, Vivek Modi, R. Gonzalo Parra, Gerardo Pepe16, Damiano Piovesan, Jaime Prilusky, Valeria Putignano, Leandro G. Radusky, Pathmanaban Ramasamy, Atilio O. Rausch, Nathalie Reuter, Luis A. Rodriguez, Nathan J Rollins, Antonio Rosato, Paweł Rubach, Luis Serrano, Gulzar Singh,Petr Skoda, Carlos Oscar S. Sorzano, Jan Stourac, Joanna I Sulkowska, Radka Svobodova, Natalia Tichshenko, Silvio C.E. Tosatto, Wim Vranken, Mark N Wass, Dandan Xue, Daniel Zaidman, Janet Thornton, Michael Sternberg, Christine Orengo, Sameer VelankarPostprint (published version
Pulchroteratura huiqing Tan, Gorochov & Wahab 2017
No full textPulchroteratura huiqing Tan, Gorochov & Wahab, 2017 (Fig. 5) http://lsid.speciesfile.org/urn:lsid: Orthoptera.speciesfile.org:TaxonName:499451 Material examined. 1 female (KB.17.88), Brunei Darussalam, Ulu Temburong National Park, Kuala Belalong Field Studies Centre along Ashton Trail, primary ridge dipterocarp forest, N4.54636, E115.15682, 136.8± 7.1 m.a.s.l., under foliage of tree, 27 July 2017, 1850 hours, coll. M. K. Tan; 1 female (KB.17.101), same locality, near Sungei Mata Ikan, N4.54697, E115.15701, 133.0± 7.9 m.a.s.l., under foliage of tree, 28 July 2017, 1855 hours, coll. M. K. Tan (all dried pinned, ZRC). Female description. Similar to male in habitus (Fig. 5A). Tenth abdominal tergite with posterior margin truncated, in the middle produced into a tongue-shaped flat process with obtuse apex (Fig. 5B). Epiproct small and rounded, concealed by the flat process of tenth abdominal tergite (Fig. 5B). Cercus longer and slender, cylindrical before tapering to an acute apex. Subgenital plate small and very short, transverse, much wider than long; with posterior margin notched in the middle (Fig. 5C). Ovipositor fairly stout, with base slightly swollen, wider than in the middle; with middle third narrow, dorsal and ventral margins parallel; with apical third wider than middle third (Fig. 5D). Base of ovipositor with a rectangular lateral plate (lp) on the dorsal valve (when viewed in profile), longer than tall, slightly swollen (Fig. 5D); with a small dorso-lateral lamellate lobe (dll) on each side above the basal margin of the lateral plate, pointing dorsad with apex obtuse (Fig. 5D); with a small ventro-lateral triangular lamellate lobe (vll) extending laterally outwards (when viewed ventrally) (Fig. 5C). Valves of ovipositor smooth (ventral valve feebly denticulated at the apex), with margins distinctly sclerotized near the apex (Fig. 5D); ventral valve shorter than dorsal valve, forming a small and stout hook at the apex; apex of ventral hook truncated; dorsal valve tapers to an acute apex (Fig. 5E). Colouration. Similar to male. Measurement (in mm). BL = 8.3, BWL = 19.9, PL = 3.0, TL = 17.0, HWT = 0.0, HFL = 11.1, HTL = 14.1, OL = 5.4.Published as part of Tan, Ming Kai & Wahab, Rodzay Bin Haji Abdul, 2018, New taxa and notes of katydids from the tribe Meconematini (Orthoptera: Meconematinae) from Brunei Darussalam (Part 2), pp. 582-590 in Zootaxa 4407 (4) on pages 589-590, DOI: 10.11646/zootaxa.4407.4.10, http://zenodo.org/record/122103
Efeito citotóxico do óxido nítrico e do taxol em células linfoblásticas leucêmicas: envolvimento do fator de transcrição NF-kB e papel da glutationa
No full textTese (doutorado) - Universidade Federal de Santa Catarina, Centro de Ciências Biológicas. Programa de Pós-Graduação em Farmacologia.O presente trabalho avaliou, através de técnicas moleculares, bioquímicas e farmacológicas, o efeito citotóxico do óxido nítrico (NO) e do taxol sobre células linfoblásticas leucêmicas. Foi investigado o envolvimento do NF-kB e a importância da glutationa na citotoxicidade causada pelo NO e pelo taxol. Os resultados obtidos, demonstraram que o efeito citotóxico do NO e do taxol sobre células leucêmicas linfoblásticas parecem atuar em vias muito semelhantes, ou seja, ambos apresentaram ações independentes de alterações no citoesqueleto, inibiram a atividade do NF-kB e depletaram os níveis de glutationa (GSH). Além disso, quando associados, apresentaram efeito citotóxico sinérgico. Sendo assim, concluímos que o NO e o taxol, além de diminuírem os níveis de glutationa intracelular, o que sensibiliza as células aos danos oxidativos e nitrosativos, também impedem o restabelecimento dos níveis normais de GSH intracelular, através da inibição da atividade do NF-kB
Magyarországi diákok a bécsi egyetemen 1365–1526. Students from Hungary at the University of Vienna 1365–1526
No full textA deletion spanning the promoter and first exon of the hair cycle-specific ASIP transcript isoform in black and tan rabbits.
No full textBlack and tan animals have tan-coloured ventral body surfaces separated by sharp boundaries from black-coloured dorsal body surfaces. In the at mouse mutant, a retroviral 6 kb insertion located in the hair cycle-specific promoter of the murine Asip gene encoding agouti signalling protein causes the black and tan phenotype. In rabbits, three ASIP alleles are thought to exist, including an at allele causing a black and tan coat colour that closely resembles the mouse black and tan phenotype. The goal of our study was to identify the functional genetic variant causing the rabbit at allele. We performed a WGS-based comparative analysis of the ASIP gene in one black and tan and three wt agouti-coloured rabbits. The analysis identified 75 at -associated variants including an 11 kb deletion. The deletion is located in the region of the hair cycle-specific ASIP promoter and thus in a region homologous to the site of the retroviral insertion causing the at allele in mice. We observed perfect association of the genotypes at this deletion with the coat colour phenotype in 49 rabbits. The comparative analysis and the previous knowledge about the regulation of ASIP expression suggest that the 11 kb deletion is the most likely causative variant for the black and tan phenotype in rabbits
Role of SUMO-1 modification in transcriptional activation
No full textIn unstimulated cells, the transcription factor NF-κB is held in the
cytoplasm in an inactive state by IκB inhibitor proteins. Activation of NF--KB is
mediated by signal induced degradation of IκBα via the ubiquitin proteasome-dependent
pathway. Targeting the proteins for ubiquitin-mediated proteolysis is an
irrevocable decision, and as such, the process needs to be highly specific and tightly
regulated. This task is achieved by conjugation and deconjugation enzymes that act
in a dynamic and coordinated mechanism.
In a yeast two hybrid screen designed to identify proteins involved in IκBα
signalling Ubch9 was found to interact with the N-terminal regulatory region of
IκBα. Although Ubch9 is an enzyme homologous to E2 ubiquitin conjugating
enzymes we have shown that is unable to form a thioester with ubiquitin but it is
capable to form a thioester with the small ubiquitin-like protein SUMO- 1. To fully
characterise the SUMO-1 modification reaction we have purified the proteins and
cloned the genes encoding the SUMO-1 activating enzyme (SAEl/SAE2) and
shown that it is homologous to enzymes involved in the activation of ubiquitin,
Smt3p, the yeast SUMO-1 homologue, and Rublp/Nedd8, another ubiquitin-like
protein. SUMO-1 is conjugated to target proteins by a pathway that is distinct from,
but analogous to, ubiquitin conjugation.
SUMO-1 was efficiently conjugated, both in vivo and in vitro, to IκBα on
lysine 21, which is also utilised for ubiquitin modification. Thus, by blocking
ubiquitination SUMO-1 modification acts antagonistically to generate a pool of
IκBα resistant to proteasome-mediated degradation which consequently inhibits
NF-κB dependent transcription activation.
In view of several lines of similarity between NF-kB and p53, the
involvement of SUMO-1 modification in the metabolism of the tumour supressor
p53 was investigated. We have shown that p53 is modified by SUMO-1 at a single
site, lysine 386 in the C-terminus of p53. Although p53 is regulated by
ubiquitination, SUMO-1 and ubiquitin modification do not compete for the same
lysine in p53. However, overexpression of SUMO-1 activates the transcriptional
activity of wild type p53, but not K386R p53 where the SUMO-1 acceptor site has
been mutated.
A consensus sequence was obtained by comparison of the sequences
surrounding the SUMO-1 acceptor lysine in proteins that have been shown to be
modified by SUMO-1 and revealed a possible recognition site for SUMO-1
conjugation machinery.
Tagging of proteins with SUMO-1 regulates transcriptional activation, either
by interfering with subcellular location or with the ubiquitination pathway. The
pathway may represent a novel target for drug development
- …
